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Biochemistry - Nucleic Acids and Protein Synthesis
Biochemistry - Nucleic Acids and Protein Synthesis
Biochemistry - Nucleic Acids and Protein Synthesis
Protein Synthesis
Introduction
Backbones of chromosomes
Phosphate
Bases
N H2 O O
4
CH3
3 N 5 N HN HN
2 6
N O N O N O N
1
H H H
Pyrimidine Cytosine (C) Thymine (T) Uracil (U)
(DNA and (DNA only) (in RNA only)
some RNA)
6 7 N H2 O
1 5 N
N N N HN N
8
2 N9
N 4 N N H2N N N
3
H H H
Purine Adenine (A) Guanine (G)
(DNA and RNA) (DNA and RNA)
Sugars (monosaccharide)
RNA contains:
• D-Ribose sugar
DNA contains:
• 2-Deoxy-D-Ribose sugar (without O on carbon 2)
Nucleoside
O O
uracil O
CH3
HN
HN
N O N -D -ribos ide 1
H H 5' O N a -N -glycosid ic
hymine (T) Uracil (U)
HOCH2 O bonß-N-glycosidic
d bond
1'
NA only) (in RNA only) 4' H H
H 3' 2' H anomeric
HO OH carb on
O
Urid ine
HN N
Nucleoside
To name a nucleoside derived from a pyrimidine base, use the suffix ―-idine‖.
To name a nucleoside derived from a purine base, use the suffix ―-osine‖.
For deoxyribonucleosides, add the prefix ―deoxy-‖.
Nucleotide
NH2 NH2
Phosphate ester bond
N N
O O O O N
N 5’
5’
O- P OH + HO CH2 O- P O CH2
O O
-
O- 1’ O
OH OH
Phosphodiester
bond
Sequence of nucleotides.
Base sequence is read from the C5’ (free phosphate) end to the C3’ (free hydroxyl) end.
-ACGU-
Secondary structure of DNA
Adenine-Thymine (A–T)
Guanine-Cytosine (G-C)
• Sugar-Phosphate backbone is
hydrophilic and stays on the outside
(bases are hydrophobic).
3’ 5’
Secondary structure of DNA
Chromatin:
Condensed nucleosomes
Higher structure of DNA
Chromatin fibers are organized into loops, and the loops into the bands
that provide the superstructure of chromosomes.
Chromosome & Gene
- A gene is the portion of the DNA molecule responsible for the synthesis
of a single protein (1000 to 2000 nucleotides).
Difference between DNA & RNA
By breaking H-bonds
Replication
Component Function
Helicase Unwinds the DNA double helix
Primase Synthesiz es primers
Clamp prote in Threads leading strand
DNA polymerase Joins assembled nucleotide s
Ligase Joins Okazaki fragments in
lagging strand
Helicases
Translation
DNA RNA
replication replication
Reverse
Reversetranscriptase
transcription
Transcription
Begins when the section of a DNA that contains the gene to be copied unwinds.
Direction of transcription
RNA Polymerase
From the template strand of DNA below, write out the mRNA and
informational strand of DNA sequences:
mRNA (as a carrier molecule) moves out of the nucleus and goes to ribosomes.
Overall function of RAN’s in the cell: facilitate the task of synthesizing protein.
Genetic code
5' U C A G 3'
UUU Phe UCU Ser U AU Tyr U GU Cys U
UUC Phe UCC Ser U AC Tyr U GC Cys C
U UUA Leu UCA Ser U AA Stop U GA S top A
UUG Leu UCG Ser U AG Stop U GG Trp G
CUU Leu CCU Pro CAU His CGU Arg U
CUC Leu CCC Pro CAC His CGC Arg C
C CUA Leu CCA Pro CAA Gln CGA Arg A
CUG Leu CCG Pro CAG Gln CGG Arg G
AU U Ile ACU Thr AAU As n A GU Ser U
As n C
A AU C Ile ACC Thr AAC A GC Ser
A
AU A Ile ACA Thr AAA Lys A GA Arg
AU G Met* ACG Thr AAG Lys A GG Arg G
GU U Val GCU Ala GAU A sp GGU Gly U
Val Ala A sp Gly
G GU C GCC GAC GGC C
GU A Val GCA Ala GAA Glu GGA Gly A
GU G Val GCG Ala GAG Glu GGG Gly G
*AUG s ign als tran slation initiation as w ell as codin g for Met
Genetic code
•Codons are written from the 5’ end to the 3’ end of the mRNA molecule
1. Signals the start of the proteins synthesis (at the beginning of an mRNA).
2. Specifies the amino acid methionine (Met) (in the middle of an mRNA).
tRNA (transfer RNA)
Anticodon loop
A G U
Codon on mRNA U C A
Transcription
Translation
Protein synthesis
• Peptide bonds form between an amino acid and the end of the
growing peptide chain.
• The ribosome moves along mRNA until the end of the codon
(translocation).
5' U C A G 3'
C A G 3'
Ribosome UUU
encounters a Phe
stop UCU
condon. Ser U AU Tyr U GU Cys U
Phe UCU Ser U AU
UUCTyr Phe U GU UCCCys Ser U U AC Tyr U GC Cys C
Phe UCC Ser U U ACUUATyr Leu U GC
UCACys Ser C U AA Stop U GA S top A
Leu UCA Ser U AA
UUG Stop
Leu U GA Ser A U AG Stop
UCGS top U GG Trp G
Leu UCG Ser U AG Stop U GG Trp G
CUU Leu CCU Pro CAU His CGU Arg U
Leu CCU Pro CAU His
CUC Leu CGU CCCArg Pro U CAC His CGC Arg C
Leu No tRNA to complement
CCC Pro C CAC CUA the termination
HisLeu CGC CCAArg codon.
Pro C CAA Gln CGA Arg A
Leu CCA Pro CAACUGGln Leu CGA CCGArg Pro A CAG Gln CGG Arg G
Leu CCG Pro CAG Gln CGG Arg G
AU U Ile ACU Thr AAU As n A GU Ser U
Ile An enzyme
ACU Thr releases
AAUAU
the
C
complete
AsIle
n A GU
ACC
polypeptide
SerThr
chain
U AAC As n from the ribosome.
A GC Ser C
A AsIle
n
Ile ACC Thr AACAU A A GC
ACASer Thr C AAA Lys A GA Arg A
Ile ACA Thr AAAAU GLysMet*A GA ACGArg Thr A AAG Lys A GG Arg G
Met* ACG Thr AAG Lys A GG Arg G
GU U Val GCU Ala GAU A sp GGU Gly U
Val GCU Ala GAUGU CA sp
Val GGUGCC GlyAla Ustructure
GAC A(active
sp GGC Gly C
Amino acids G form the three-dimensional protein).
Val GCC Ala GACGU AA sp
Val GGC GCAGly Ala C GAA Glu GGA Gly A
Val GCA Ala GAA GluVal GGA
GU G GCGGly Ala A GAG Glu GGG Gly G
Val GCG Ala GAG Glu GGG Gly G
*AUG s ign als tran slation initiation as w ell as codin g for Met
ign als tran slation initiation as w ell as codin g for Met
Translation
There are 3 stages in translation:
Altered DNA will be limited to that cell and its daughter cells. Cancer
Frameshift Mutation
One or more bases is/are added to or deleted from
the normal order of bases in DNA.
In hemoglobin, substitution of just one amino acid can result in the fatal
disease sickle cell anemia.
No more amino acids are added. A need protein is not synthesized. The
organism may die.
Frameshift Mutation
Combining the two pieces of DNA (with DNA ligase enzyme) forms DNA
containing the new segment.
•Any type of cell (skin, saliva, semen, blood, etc.) can be used to
obtain a DNA fingerprint.
•The DNA is first amplified by PCR, and then cut into fragments
by restriction enzymes.
DNA fragments can be visualized on X-ray film after they have been
separated:
Viruses
Reverse transcriptase
Viruses
The viral DNA can then transcribe RNA, which then directs
protein synthesis (new retroviral particles to infect other cells).